RLMD_PHOAS
ID RLMD_PHOAS Reviewed; 220 AA.
AC P55136;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
DE EC=2.1.1.190;
DE AltName: Full=23S rRNA(m5U1939)-methyltransferase;
DE Flags: Fragment;
GN Name=rlmD; Synonyms=rumA;
OS Photobacterium angustum (strain S14 / CCUG 15956) (Vibrio sp. (strain S14 /
OS CCUG 15956)).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Photobacterium.
OX NCBI_TaxID=314292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7928955; DOI=10.1128/jb.176.19.5949-5957.1994;
RA Flaerdh K., Axberg T., Albertson N.H., Kjelleberg S.;
RT "Stringent control during carbon starvation of marine Vibrio sp. strain
RT S14: molecular cloning, nucleotide sequence, and deletion of the relA
RT gene.";
RL J. Bacteriol. 176:5949-5957(1994).
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 1939
CC (m5U1939) in 23S rRNA. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-adenosyl-L-methionine + uridine(1939) in 23S rRNA = 5-
CC methyluridine(1939) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42908, Rhea:RHEA-COMP:10278, Rhea:RHEA-COMP:10279,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.190;
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. RlmD subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU01024}.
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DR EMBL; U13769; AAA62209.1; -; Genomic_DNA.
DR AlphaFoldDB; P55136; -.
DR SMR; P55136; -.
DR STRING; 314292.VAS14_20406; -.
DR eggNOG; COG2265; Bacteria.
DR GO; GO:0008173; F:RNA methyltransferase activity; IEA:InterPro.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR030390; MeTrfase_TrmA_AS.
DR InterPro; IPR030391; MeTrfase_TrmA_CS.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR010280; U5_MeTrfase_fam.
DR PANTHER; PTHR11061; PTHR11061; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
DR PROSITE; PS01230; TRMA_1; 1.
DR PROSITE; PS01231; TRMA_2; 1.
PE 3: Inferred from homology;
KW Methyltransferase; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN <1..220
FT /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT /id="PRO_0000161918"
FT ACT_SITE 167
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 43
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 72
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 77
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 93
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 120
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 141
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT NON_TER 1
SQ SEQUENCE 220 AA; 24490 MW; 93FB73DDC394412B CRC64;
QLNMALMLFL APSSDELDHV LGEQPYYDID DVRLTFSPKD FIQVNRDVNV KMVEQAINWL
DIQPQDRVLD LFCGLGNFSL PLARRAKAVV GVEGVDEMVA RATANAAANG LDNATFYQAN
LDEDVTKLVW AQEQFDKILL DPARAGAAGV MQHIVNLAPS KVVYVSCNPA TLARDSQMLL
QQGYKLARLG MMDMFPHTGH LESMTLFVKT NHHKKNSNVM
